Opportunities and challenges of macrogenetic studies

Nature Reviews Genetics, Год журнала: 2021, Номер 22(12), С. 791 - 807

Опубликована: Авг. 18, 2021

Язык: Английский

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Genomics for monitoring and understanding species responses to global climate change

Nature Reviews Genetics, Год журнала: 2023, Номер 25(3), С. 165 - 183

Опубликована: Окт. 20, 2023

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish species' potential adapt future environments. Understanding monitoring how organisms respond human-driven change is therefore major priority for conservation rapidly changing environment. Recent developments genomic, transcriptomic epigenomic technologies enabling unprecedented insights into evolutionary processes molecular bases adaptation. This Review summarizes methods that apply integrate omics tools experimentally investigate, monitor predict species communities wild cope with change, which by genetically adapting new conditions, through range shifts or phenotypic plasticity. We identify advantages limitations each method discuss research avenues would improve our understanding responses highlighting need holistic, multi-omics approaches ecosystem during Species can shifting their these responses.

Язык: Английский

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Systematic conservation prioritization with the prioritizr R package

Conservation Biology, Год журнала: 2024, Номер unknown

Опубликована: Сен. 13, 2024

Abstract Plans for expanding protected area systems (prioritizations) need to fulfill conservation objectives. They also account other factors, such as economic feasibility and anthropogenic land‐use requirements. Although prioritizations are often generated with decision support tools, most tools have limitations that hinder their use decision‐making. We outlined how the prioritizr R package ( https://prioritizr.net ) can be used systematic prioritization. This tool provides a flexible interface build planning problems. It leverage variety of commercial (e.g., Gurobi) open‐source CBC SYMPHONY) exact algorithm solvers identify optimal solutions in short period. is compatible spatially explicit ESRI Shapefile, GeoTIFF) nonspatial tabular Microsoft Excel Spreadsheet) data formats. Additionally, it functionality evaluating prioritizations, assessing relative importance different places selected by To showcase package, we applied case study based Washington state (United States) which developed prioritization improve coverage native avifauna. accounted land acquisition costs, existing areas, might not suitable establishment, spatial fragmentation. conducted benchmark analysis examine performance solvers. The identified 12,400 km 2 priority areas increasing percentage species’ distributions covered areas. open source were able quickly solve large‐scale problems, required complex, problems.. available on Comprehensive Archive Network (CRAN). In addition reserve selection, inform habitat restoration, connectivity enhancement, ecosystem service provisioning. has been numerous exercises best practices aid real‐world

Язык: Английский

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Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest

Evolutionary Applications, Год журнала: 2022, Номер 15(3), С. 403 - 416

Опубликована: Фев. 4, 2022

Gradient Forest (GF) is a machine learning algorithm designed to analyze spatial patterns of biodiversity as function environmental gradients. An offset measure between the GF-predicted association adapted alleles and new environment (GF Offset) increasingly being used predict loss environmentally under rapid change, but remains mostly untested for this purpose. Here, we explore robustness GF Offset assumption violations, its relationship measures fitness, using SLiM simulations with explicit genome architecture metapopulation. We evaluate in: (1) neutral model no adaptation; (2) monogenic "population genetic" single locus; (3) polygenic "quantitative two adaptive traits, each adapting different environment. found be broadly correlated fitness offsets both locus architectures. However, demography, genomic architecture, nature can all confound relationships fitness. promising tool, it important understand limitations underlying assumptions, especially when in context predicting maladaptation.

Язык: Английский

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Molecular ecology meets systematic conservation planning

Trends in Ecology & Evolution, Год журнала: 2022, Номер 38(2), С. 143 - 155

Опубликована: Окт. 6, 2022

Molecular ecology (ME) and systematic conservation planning (SCP) have seen rapid technological advancements in recent decades, but the use of molecular data to conserve different aspects biodiversity remains operationally illusive.Here, core principles ME SCP are combined a novel way, showcasing how themes corresponding types from each field can complement other.A framework, including five practical steps, is provided guide both ecologists planners build plans that effectively integrate evolutionary features. Integrative proactive approaches critical long-term persistence biodiversity. provide important information on processes necessary for conserving multiple levels (genes, populations, species, ecosystems). However, rarely used spatial decision-making. Here, we bridge fields (the 'why') foundation inclusion into tools 'how'), implementing this integrative approach ecologists. The proposed framework enhances interdisciplinary capacity, which crucial achieving ambitious global goals envisioned next decade. world facing an anthropogenically driven crisis [1.Díaz S.M. et al.The Global Assessment Report Biodiversity Ecosystem Services: Summary Policy Makers. Intergovernmental Science-Policy Platform Services, 2019Google Scholar,2.Sippel S. al.Climate change now detectable any single day weather at scale.Nat. Clim. Chang. 2020; 10: 35-41Crossref Scopus (134) Google Scholar] must be urgently addressed restore ecosystem functions, mitigate climate change, maintain human well-being [3.Arneth A. al.Post-2020 targets need embrace change.Proc. Natl. Acad. Sci. U. 117: 30882-30891Crossref PubMed (115) Scholar,4.Leclère D. al.Bending curve terrestrial needs integrated strategy.Nature. 585: 551-556Crossref (343) Scholar]. Protected area establishment cornerstone conservation. protected system coverage has been increasing, marine ecosystems [5.Bingham H.C. al.Sixty years tracking progress using World Database Areas.Nat. Ecol. Evol. 2019; 3: 737-743Crossref (56) incomplete falls short safeguarding all [genes, populations (see Glossary), ecosystems] [6.Visconti P. al.Protected post-2020.Science. 2021; 364: 239-241Crossref (227) Consequently, actions needed places will promote resilience, adaptive potential, species changing [7.Des Roches al.Conserving intraspecific variation nature's contributions people.Nat. 5: 574-582Crossref (66) Over past 30 years, scientists rallied inform (ME [8.Avise J.C. al.Intraspecific phylogeography: mitochondrial DNA between population genetics systematics.Annu. Rev. Syst. 1987; 18: 489-522Crossref Scholar,9.Luikart G. power promise genomics: genotyping genome typing.Nat. Genet. 2003; 4: 981-994Crossref (981) Scholar]) developed as describing non-model/wild their within ecological context. Meanwhile, (SCP [10.Margules C.R. Pressey R.L. Systematic planning.Nature. 2000; 405: 243-253Crossref (4207) Scholar,11.Kirkpatrick J.B. An iterative method establishing priorities selection nature reserves: example Tasmania.Biol. Cons. 1983; 25: 127-134Crossref (379) emerged transparent, reproducible, quantitative identifying cost-effective priority areas As these continue develop, there growing acceptance they should decisions relevant objectives [12.Hoban al.Global commitments monitoring genetic diversity feasible.BioScience. 71: 964-976Crossref (67) Several subdisciplines suitable SCP, such extinction probabilities or landscape connectivity [13.Zizka al.Existing future directions link macroecology, macroevolution prioritization.Ecography. 6e05557Google Recent work described most highlighting diversity, dispersal, effective sizes (Ne) [14.Andrello M. al.Evolving prioritization with data.Trends 2022; 37: 553-564Abstract Full Text PDF (17) little guidance exists enable practitioners navigate when management, implement various genetic/genomic software, assess well being met [15.Holderegger R. al.Conservation genetics: linking science practice.Mol. 28: 3848-3856Crossref (68) present novel, reconciles identify Our ensures ecologically driven, meet criteria real-world implementation. To achieve this, concepts, themes, shared understanding decision-making 'why' section). We then outline procedures for: (i) defining objectives; (ii) collection; (iii) calculate metrics; spatially interpolate (iv) them 'how' grounded spatiotemporal natural offers metrics fundamental assessing, conserving, [16.Hoban status trends: towards suite Essential Variables (EBVs) composition.Biol. 97: 1511-1538Crossref (50) Major strong focus connectivity, differentiation, demography (hereafter, 'CADDD'). Connectivity describes level gene flow across distributional range, source/sink dynamics; potential refers variance potentially derived local selective pressures pertain genomic vulnerability its resilience environmental changes (here restrict definition relate amounts/frequencies genes assumed functions); represents extant (putatively neutral adaptive); differentiation relative degree isolation measured by differences allele frequencies among individuals clusters (populations); includes inbreeding Ne, historical both. Thus, CADDD encompasses putatively loci assuring Scholar,17.von der Heyden Making history count: coral reef fishes processes.Coral Reefs. 2017; 36: 183-194Crossref (23) Scholar,18.Clark R.D. al.Genomic signatures divergent clownfish range margins.Proc. Soc. B Biol. 288: 20210407Crossref (3) propose offer more clarity about whether objectives. concerned optimal application explicit management representation Scholar,19.Watson J.E.M. al.Systematic planning: past, future.Conserv. Biogeogr. 2011; 1: 136-160Crossref (90) It involves generating prioritizations sites objectives, while accounting social, economic, political constraints efficiently. Conservation objective examples include habitat threatened restoring isolated securing comprehensive Achieving requires clear choices ecosystems) facets (taxonomic, phylogenetic, functional) included [20.Carvalho S.B. al.Spatial spanning continuum.Nat. 0151Crossref (64) Scholar,21.Pollock L.J. al.Protecting (in complexity): new models methods.Trends 35: 1119-1128Abstract (79) dividing region units, calculating amount feature one, sets units goals. ensure feasible implementation, accounts economic opportunity costs, resource-use requirements (e.g., ensuring sufficient agricultural production recreational fishing [22.Moilanen Prioritization: Quantitative Methods Computational Tools. Oxford University Press, 2009Crossref Scholar]). maximize efficiency algorithms developed, Marxan [23.Ball I.R. al.Marxan relatives: software prioritisation.in: Moilanen Spatial Prioritisation: 2009: 185-195Google Scholar], Zonation [24.Moilanen al.Zonation—Spatial Planning Software. Version 4. User Manual. C-BIG Biology Informatics Group, 2014Google prioritizr R package [25.Hanson J.O. al.Prioritizr: Prioritization Package 4.1. 5. Project, 2020Google (Box 1). set decision-making, easily (Figure 1 Table Comprehensiveness sample main components interest ecoregions, types, species). insights comprehensiveness phylogenetic [26.Owen N.R. captures than just functional diversity.Nat. Commun. 859Crossref (63) find best represent lineages, [27.Rosauer D.F. al.Real-world Kimberley, Australia, sidesteps uncertain taxonomy.Conserv. Lett. 2018; 11e12438Crossref (32) Adequacy ability network viability habitats. adequacy, significant (ESUs), measuring quantifying estimating Ne [28.Corlett R.T. A bigger toolbox: biotechnology conservation.Trends Biotechnol. 55-65Abstract (91) Representativeness capture full variety areas, ideally biological organization. imperative assure suitably represented, instance, prioritizing ESU private alleles [29.Nielsen E.S. al.Multispecies planning.Conserv. 31: 872-882Crossref (38) Scholar,30.Paz-Vinas I. diversity.Proc. 285: 20172746Crossref (52) distinguish interspecific applying comprehensiveness, measures number populations) representativeness. Efficiency highlights consider costs foregone commercial activities [31.Watson K.B. al.Effects demand services.Conserv. 33: 942-952Crossref While unlikely contribute directly reserve efficiency, it facilitate providing procedures. relates counteract fragmentation protect corridors underpin functioning [32.Keeley A.T.H. al.Thirty assessment factors influencing plan implementation.Environ. Res. 14103001Crossref (60) connected lead demographic benefits metapopulations [33.Keeley al.Connectivity monitoring.Biol. Conserv. 255109008Crossref Scholar].Box 1Conservation decision support toolsCurrently, commonly Marxan, Zonation, Scholar, 24.Moilanen 25.Hanson These frame mathematical optimization problems solve generate prioritizations. Both import formats ESRI Shapefile GeoTIFF). Additional CLUZ QMarxan [88.Smith plugin QGIS: designing systems other networks.RIO. 5e33510Crossref Scholar]iii, available assist processing (step 4 'The how' In addition, Connect [70.Daigle R.M. al.Operationalizing Connect.Methods 11: 570-579Crossref (55) general-purpose tool enables inputting (i.e., animal tracking/dispersal data), genetic, structural resistance) features prioritizations.Each uses formulations express problems. For example, minimum formulation wherein goal 'cheapest' actions, expected meets threshold (termed 'representation target'). budget-limited overall feature, total cost does not exceed budget threshold. Finally, allows users create custom-built problem (including formulations). Additionally, tools, except (but see Zones [89.Watts M.E. Zones: based land- sea-use zoning.Environ. Model. Softw. 2009; 24: 1513-1521Crossref (421) Scholar]), accommodate zones.These also backward heuristic algorithm iteratively rank such, thresholds often imposed top 20% ranked units). simulated annealing algorithm, compared Although could prioritizations, do guarantee optimality [90.Hanson al.Optimality projects.Methods 1655-1663Crossref (15) Non-optimal solutions misdirect resources inefficiencies. overcome limitation, exact algorithms, flexibility quickly stakeholder negotiations Scholar,24.Moilanen Scholar].Table 1Matching fieldsaThis table specific ways intersect, respective (PA) systems.Conservation principlesMolecular principlesConnectivity (gene flow)Adaptive capacityDiversityDifferentiationDemographyComprehensive : PA contain broad biotic elements etc.)(a)(b)(c)OBJECTIVE: systemMETRICS:Phylogenetic endemismPhylogenetic diversity(d)OBJECTIVE: trees differencesPhylogeographic mapsPhylogenetic distinctiveness(e)Adequate: element habitat) persistence(f)(g)OBJECTIVE: probability under disturbancesMETRICS:Genomic vulnerabilityOutlier frequencyRare/private allelesPopulation index (PAI)Adaptive score (Sadapt)(h)OBJECTIVE: genetically diverse low inbreeding, high heterozygosity) METRICS:Proportion 'unit' (species, population, deme) required diversityNucleotide haplotype diversityHeterozygosityAllelic richness(i)OBJECTIVE: unique populationsMETRICS:Population structure (admixture plots)FST-based metricsGenetic distances Nei's distance)(j)OBJECTIVE: adequate stability)METRICS:NeInbreeding coefficientsDemographic simulationsRepresentative: reflects ecotypes, etc.)(k)(l)OBJECTIVE: genotypesMETRICS:Allele candidate pertaining featuresAdaptive diversityDifferently adapted lineages(m)OBJECTIVE: rare allelesMETRICS:Haplotype networksRare/private allelesNeutral clustering(n)OBJECTIVE: Represent evolutionarily populations/lineagesMETRICS:Population plots/PCAs)FST-based Genetic distancesLineage delineations(o)OBJECTIVE: dynamics metapopulation processes, adaptation, divergence)METRICS:Measures hybridization inbreedingNe growth ratesSimulated eco-evolutionary dynamicsEfficient: cost-effectiveConnectivity: linkages sites(p)OBJECTIVE: Maintain and/or enhance METRICS:Migration rates (m)Effective migrantsSlatkin's psi(q)OBJECTIVE: Ensure beneficial adaptations export represented rescue)METRICS:Allele rare/private alleles(r)OBJECTIVE: prioritized over othersMETRICS:Connectivity combination with:Nucleotide richness(s)(t)OBJECTIVE: source sink migrants populations)METRICS:Effective migrantsConnectivity measuresMigration resistance surfacesa This systems. Open tab Currently, Each zones.

Язык: Английский

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Evolving spatial conservation prioritization with intraspecific genetic data

Trends in Ecology & Evolution, Год журнала: 2022, Номер 37(6), С. 553 - 564

Опубликована: Апрель 18, 2022

Язык: Английский

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The application gap: Genomics for biodiversity and ecosystem service management

Biological Conservation, Год журнала: 2023, Номер 278, С. 109883 - 109883

Опубликована: Янв. 4, 2023

The conservation of biodiversity from the genetic to community levels is fundamental for continual provision ecosystem services (ES), benefits that ecosystems provide people. Genetic and genomic diversity enhance resilience populations communities underpin functions services. We show genomics applications are mostly limited flagship species their ES management underachieved. propose a framework on how can guide sustainable bridge this genomics-ES 'application gap'. review knowledge in single (relatedness, potentially adaptive variants) or interacting (host-microorganism coevolution, hybridization) effective actions. These include population supplementation, assisted migration hybridization promote climate-adapted variants potential, control invasives, delimitation areas, provenancing strategies restoration, managing microbial function solving trade-offs. Genomics-informed actions improved outcomes supported through synergies between scientists managers at local, regional international levels, development standardized workflows, training incorporation local information. Such facilitate implementation policies such as UN 2030 goals EU Biodiversity strategy 2030, support inclusion ambitious new CBD post-2020 Global Framework hybrids.

Язык: Английский

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Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Heredity, Год журнала: 2025, Номер unknown

Опубликована: Фев. 7, 2025

Mitonuclear discordance between species is readily documented in marine fishes. Such may either be the result of past natural phenomena or recent introgression from previously seperated after shifts their spatial distributions. Using ancient DNA spanning five millennia, we here investigate long-term presence Pacific bluefin tuna (Thunnus orientalis) and albacore alalunga) -like mitochondrial (MT) genomes Atlantic thynnus), a with extensive exploitation history observed abundance age structure. Comparing (n = 130) modern 78) MT most its range, detect no significant temporal population structure, which implies ongoing gene flow populations large effective sizes over millennia. Moreover, identify discordant haplotypes specimens up to 5000 years old find that frequency these has remained similar through time. We therefore conclude not driven by introgression. Our observations provide oldest example directly environment, highlighting utility obtain insights persistence such phenomena.

Язык: Английский

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Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa

Journal of Heredity, Год журнала: 2023, Номер 114(4), С. 300 - 311

Опубликована: Фев. 23, 2023

Abstract Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species’ range protection when implementing conservation management measures. However, current workflows identifying CUs on the basis of neutral adaptive genomic variation largely ignore information contained in patterns isolation by distance (IBD), frequently primary signal population structure highly mobile taxa, such as birds, bats, marine organisms with pelagic larval stages. While individuals located either end distribution may exhibit clear genetic, phenotypic, ecological differences, IBD produces subtle changes allele frequencies space, making it difficult to draw boundaries purposes absence discrete structure. Here, we highlight pitfalls that arise applying common methods delineating continuously distributed review existing detecting breakpoints can indicate barriers gene flow taxa. In addition, propose new framework all organisms, including those characterized continuous differentiation, suggest several possible ways harness guide decisions.

Язык: Английский

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The many pathways of climate change affecting coastal ecosystems: a case study of western Vancouver Island, Canada

FACETS, Год журнала: 2025, Номер 10, С. 1 - 18

Опубликована: Янв. 1, 2025

Climate change threatens marine ecosystems with known effects on life, including changes in metabolic rates, survival, and community structure. Based a structured literature review, we developed conceptual “pathways of effects” model that summarizes how three stressors associated climate (warming, acidification, storms) affect functional species groups the West Coast Vancouver Island, Canada. We identified 155 distinct pathways from through 12 categories biological ranging biochemistry individual organisms to composition. Most were affected by several via many pathways, although studies generally considered only small fraction relevant pathways. These depended interest geographical location, highlighting importance local research. exert complex, sometimes contradictory vary across ecological scales. For example, some adversely laboratory appeared beneficial community-scale field studies. Pathways models are helpful tools summarize scientific Compiling them standardized databases would allow researchers practitioners search regions better support ecosystem-based management environmental impact assessment.

Язык: Английский

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